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Interpretive Summary: Mapping genes that affect a quantitative trait [quantitative trait loci (QTL)] of domestic animals requires a set of resource families with designed structure, sufficient DNA supply, and records for the trait. The design of resource families affects the statistical efficiency of QTL detection and is critical to the success of QTL mapping. For crossing between inbred or noninbred lines, designs that involve 1-way backcrosses, reciprocal backcrosses, or 2nd generation (F-2) crosses are possible. For inbred lines, the F-2 design is twice as efficient as backcross designs for QTL detection. Crossing between noninbred lines is a suitable design for species for which inbred lines are costly to produce but generally is less efficient than crossing between inbred lines. A design using a segregating population requires no crossing and, thus, minimal time and cost for establishing resource families even for species with long generation intervals. However, this design is less efficient for QTL detection than crossing designs. Based on information about QTL location, genetic markers linked to the QTL could be used for marker-assisted selection of quantitative traits, such as milk yield efficiency or mastitis resistance, and the QTL responsible for the quantitative trait could be characterized, thus allowing breeders to select directly for the QTL to improve the quantitative trait.

Technical Abstract: Mapping quantitative trait loci (QTL) requires a set of resource families with designed structure, sufficient DNA supply, and records for the trait. The design of resource families affects the statistical efficiency of QTL detection and is critical to the success of QTL mapping. Designs of resource families feasible for QTL mapping in domestic animals can be categorized into crossing between inbred lines, crossing between noninbred lines, and segregating populations. Relative efficiency of two designs is measured by the ratio of sample sizes required for QTL detection. For crossing between inbred or noninbred lines, 1-way backcross, reciprocal backcross, and F-2 designs are possible. The 1-way backcross design is affected by the quantitative trait's dominance effect, whereas the reciprocal backcross design is not. For crossing between inbred lines, only 1 parent provides information for QTL detection in the 1-way and reciprocal backcross designs; in contrast, 2 parents provide information in the F-2 design, which makes the F-2 design twice as efficient as backcross designs for QTL detection. Crossing between noninbred lines is a suitable design for species for which inbred lines are costly to produce but is less efficient than crossing between inbred lines unless the marker's polymorphic information content is greater than the probability that the two inbred lines do not share the same homozygous marker genotype. A segregating population requires no crossing and, thus, minimal time and cost for establishing resource families even for species with long generation intervals. However, this design is less efficient for QTL detection than crossing designs because QTL parent heterozygosity is not guaranteed and multiple QTL alleles may be responsible for QTL variation.